# HG changeset patch
# User iuc
# Date 1575463475 18000
# Node ID 4d343c1f606bff0c7efa2c5d8e8c29f8eef64419
# Parent  04866f817daaa250fbbf5287aca6c8863c1cd69e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"

diff -r 04866f817daa -r 4d343c1f606b bamtools.xml
--- a/bamtools.xml	Wed Jan 18 11:47:11 2017 -0500
+++ b/bamtools.xml	Wed Dec 04 07:44:35 2019 -0500
@@ -1,76 +1,69 @@
 <?xml version="1.0"?>
-<tool id="bamtools" name="Convert, Merge, Randomize" version="2.4.0">
+<tool id="bamtools" name="Convert, Merge, Randomize" version="@VERSION@.0">
     <description>BAM datasets and perform other transformations</description>
-    <requirements>
-        <requirement type="package" version="2.4.0">bamtools</requirement>
-        <requirement type="package" version="1.3.1">samtools</requirement>
-    </requirements>
-    <stdio>
-        <exit_code range="1:" />
-    </stdio>
-    <command>
+    <macros>
+          <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code">
         <![CDATA[
             ##set up input files
-            #for $bam_count, $input_bam in enumerate( $input_bams ):
-                ln -s "${input_bam}" "localbam_${bam_count}.bam" &&
-                ln -s "${input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" &&
-            #end for
-            #if str( $analysis_type.analysis_type_selector ) == "convert":
-                #if str( $analysis_type.format_type.format_type_selector ) == "pileup":
-                    #set $reference_fasta_filename = "localref.fa"
-                    #if str( $analysis_type.format_type.reference_source.reference_source_selector ) == "history":
-                        ln -s "${analysis_type.format_type.reference_source.ref_file}" "${reference_fasta_filename}" &&
-                        samtools faidx "${reference_fasta_filename}" 2>&1 || echo "Error running samtools faidx for bamtools convert" >&2 &&
+            ln -s '${input_bams}' localbam.bam &&
+            ln -s '${input_bams.metadata.bam_index}' localbam.bam.bai &&
+            #if str( $analysis_type.analysis_type_selector ) == 'convert':
+                #if str( $analysis_type.format_type.format_type_selector ) == 'pileup':
+                    #set $reference_fasta_filename = 'localref.fa'
+                    #if str( $analysis_type.format_type.reference_source.reference_source_selector ) == 'history':
+                        ln -s '${analysis_type.format_type.reference_source.ref_file}' '${reference_fasta_filename}' &&
+                        samtools faidx '${reference_fasta_filename}' 2>&1 || echo 'Error running samtools faidx for bamtools convert' >&2 &&
                     #else:
                         #set $reference_fasta_filename = str( $analysis_type.format_type.reference_source.ref_file.fields.path )
                     #end if
                 #end if
             #end if
             bamtools
-            #if str( $analysis_type.analysis_type_selector ) == "convert":
+            #if str( $analysis_type.analysis_type_selector ) == 'convert':
                 convert
                 -format ${analysis_type.format_type.format_type_selector}
-                #if str( $analysis_type.format_type.format_type_selector ) == "pileup":
+                #if str( $analysis_type.format_type.format_type_selector ) == 'pileup':
                     ${analysis_type.format_type.mapqual}
-                    -fasta "${reference_fasta_filename}"
-                #elif str( $analysis_type.format_type.format_type_selector ) == "sam":
+                    -fasta '${reference_fasta_filename}'
+                #elif str( $analysis_type.format_type.format_type_selector ) == 'sam':
                     ${analysis_type.format_type.noheader}
                 #end if
-                -out $out_file1
-            #elif str( $analysis_type.analysis_type_selector ) == "count":
+                -out '$out_file1'
+            #elif str( $analysis_type.analysis_type_selector ) == 'count':
                 count
-                > $out_file1
-            #elif str( $analysis_type.analysis_type_selector ) == "coverage":
+                > '$out_file1'
+            #elif str( $analysis_type.analysis_type_selector ) == 'coverage':
                 coverage
-                -out $out_file1
-            #elif str( $analysis_type.analysis_type_selector ) == "header":
+                -out '$out_file1'
+            #elif str( $analysis_type.analysis_type_selector ) == 'header':
                 header
-                > $out_file1
-            #elif str( $analysis_type.analysis_type_selector ) == "merge":
+                > '$out_file1'
+            #elif str( $analysis_type.analysis_type_selector ) == 'merge':
                 merge
-                -out $out_file1
-            #elif str( $analysis_type.analysis_type_selector ) == "random":
+                -out '$out_file1'
+            #elif str( $analysis_type.analysis_type_selector ) == 'random':
                 random
                 -n ${analysis_type.count}
                 -seed ${analysis_type.seed}
-                -out $out_file1
-            #elif str( $analysis_type.analysis_type_selector ) == "revert":
+                -out '$out_file1'
+            #elif str( $analysis_type.analysis_type_selector ) == 'revert':
                 revert
                 ${analysis_type.keepDuplicate}
                 ${analysis_type.keepQualities}
-                -out $out_file1
-            #elif str( $analysis_type.analysis_type_selector ) == "sort":
+                -out '$out_file1'
+            #elif str( $analysis_type.analysis_type_selector ) == 'sort':
                 sort
                 ${analysis_type.byname}
-                -out $out_file1
+                -out '$out_file1'
             #end if
-            #for $bam_count, $input_bam in enumerate( $input_bams ):
-                -in "localbam_${bam_count}.bam"
-            #end for
+            -in localbam.bam
         ]]>
     </command>
     <inputs>
-        <param name="input_bams" type="data" format="bam" label="BAM dataset(s) to filter" min="1" multiple="True"/>
+        <param name="input_bams" type="data" format="bam" label="BAM dataset(s) to filter" />
         <conditional name="analysis_type">
             <param name="analysis_type_selector" type="select" label="Select BAM manipulation" help="See help below for detailed description of each tool">
                 <option value="convert">Convert</option>
@@ -153,6 +146,7 @@
                 <when input="analysis_type.format_type.format_type_selector" value="fastq" format="fastq" />
                 <when input="analysis_type.format_type.format_type_selector" value="sam" format="sam" />
                 <when input="analysis_type.format_type.format_type_selector" value="pileup" format="pileup" />
+                <when input="analysis_type.analysis_type_selector" value="count" format="tabular" />
                 <when input="analysis_type.analysis_type_selector" value="coverage" format="tabular" />
                 <when input="analysis_type.analysis_type_selector" value="merge" format="bam" />
                 <when input="analysis_type.analysis_type_selector" value="random" format="bam" />
@@ -169,22 +163,22 @@
             <param name="reference_source_selector" value="history" />
             <param name="mapqual" value="true" />
             <param name="ref_file" ftype="fasta" value="bamtools-fasta.fa"/>
-            <output name="output_bam" file="bamtools-convert-pileup.pu" />
+            <output name="out_file1" file="bamtools-convert-pileup.pu" />
         </test>
         <test>
             <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/>
             <param name="analysis_type_selector" value="count"/>
-            <output name="output_bam" file="bamtools-count.tab" />
+            <output name="out_file1" file="bamtools-count.tab" />
         </test>
         <test>
             <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/>
             <param name="analysis_type_selector" value="coverage"/>
-            <output name="output_bam" file="bamtools-coverage.tab" />
+            <output name="out_file1" file="bamtools-coverage.tab" />
         </test>
         <test>
             <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/>
             <param name="analysis_type_selector" value="header"/>
-            <output name="output_bam" file="bamtools-header.txt" />
+            <output name="out_file1" file="bamtools-header.txt" />
         </test>
     </tests>
     <help>
diff -r 04866f817daa -r 4d343c1f606b macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Wed Dec 04 07:44:35 2019 -0500
@@ -0,0 +1,15 @@
+<?xml version="1.0"?>
+<macros>
+    <token name="@VERSION@">2.4.0</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@VERSION@">bamtools</requirement>
+            <requirement type="package" version="1.4.1">samtools</requirement>
+        </requirements>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1093/bioinformatics/btr174</citation>
+        </citations>
+    </xml>
+</macros>
\ No newline at end of file